Methods for analyzing multiple parameters of individual particles in populations are of interest in a variety of contexts. In particular, the ability to analyze multiple nucleic acids, optionally in combination with one or more other parameters, on a single-cell basis within a cell population is of broad interest to commercial and academic laboratories. Various approaches to achieving this goal suffer from one or more of the following problems: the steps involved are tedious and labor-intensive, large numbers of cells may be required (e.g., on the order of 10,000 or more cells), which may not be available from the sources to be analyzed (such as tissue biopsies), and/or available techniques may be insufficiently reproducible to generate reliable results from the small amounts of target nucleic acids present in individual cells.